UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 6346: invalid continuation byte #60
Comments
|
Hi,
Can you do me a favor and update this code in your installation?
https://github.com/NCIP/ctat-mutations/blob/devel/PyLib/ctat_util.py
This should hopefully solve that error, and if you rerun the original job,
it should pick up where it left off.
thanks,
~brian
…On Tue, Sep 15, 2020 at 12:07 PM foxchase ***@***.***> wrote:
Dear ctat-mutations developers,
I tested the demo data and everything went well. when I tried my own data
I got two Traceback errors at almost the final stage:
2020-09-15 11:39:07,731: INFO Pipeliner.Pipeliner.run_cmd Running:
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
Traceback (most recent call last):
File
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py",
line 47, in
for line in hndl_vcf:
File "/home/jpei/anaconda3/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 6346:
invalid continuation byte
2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run_cmd Error: Command
'/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf'
returned non-zero exit status 1., exit val: 1
2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run Error, command: [
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
] failed, stack trace: [ st:
file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py,
lineno:86
st: file:./ctat_mutations, lineno:1364
st: file:./ctat_mutations, lineno:2816
]
Traceback (most recent call last):
File "./ctat_mutations", line 2824, in
pipeliner.run()
File
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py",
line 71, in run
cmd.run(checkpoint_dir)
File
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py",
line 132, in run
raise RuntimeError(errmsg)
RuntimeError: Error, command: [
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
] failed, stack trace: [ st:
file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py,
lineno:86
st: file:./ctat_mutations, lineno:1364
st: file:./ctat_mutations, lineno:2816
]
Thank you for your effort.
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
|
|
Hi Brian,
I did what you asked, and it went well, no Traceback now.
Thank you
…________________________________
From: Brian Haas <notifications@github.com>
Sent: Tuesday, September 15, 2020 12:45 PM
To: NCIP/ctat-mutations <ctat-mutations@noreply.github.com>
Cc: Pei, Jianming <Jianming.Pei@fccc.edu>; Author <author@noreply.github.com>
Subject: Re: [NCIP/ctat-mutations] UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 6346: invalid continuation byte (#60)
EXTERNAL MESSAGE. DO NOT open attachments or click links from unknown senders or unknown emails.
________________________________
Hi,
Can you do me a favor and update this code in your installation?
https://github.com/NCIP/ctat-mutations/blob/devel/PyLib/ctat_util.py
This should hopefully solve that error, and if you rerun the original job,
it should pick up where it left off.
thanks,
~brian
On Tue, Sep 15, 2020 at 12:07 PM foxchase ***@***.***> wrote:
Dear ctat-mutations developers,
I tested the demo data and everything went well. when I tried my own data
I got two Traceback errors at almost the final stage:
2020-09-15 11:39:07,731: INFO Pipeliner.Pipeliner.run_cmd Running:
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
Traceback (most recent call last):
File
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py",
line 47, in
for line in hndl_vcf:
File "/home/jpei/anaconda3/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 6346:
invalid continuation byte
2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run_cmd Error: Command
'/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf'
returned non-zero exit status 1., exit val: 1
2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run Error, command: [
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
] failed, stack trace: [ st:
file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py,
lineno:86
st: file:./ctat_mutations, lineno:1364
st: file:./ctat_mutations, lineno:2816
]
Traceback (most recent call last):
File "./ctat_mutations", line 2824, in
pipeliner.run()
File
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py",
line 71, in run
cmd.run(checkpoint_dir)
File
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py",
line 132, in run
raise RuntimeError(errmsg)
RuntimeError: Error, command: [
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
] failed, stack trace: [ st:
file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py,
lineno:86
st: file:./ctat_mutations, lineno:1364
st: file:./ctat_mutations, lineno:2816
]
Thank you for your effort.
—
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<#60>, or unsubscribe
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.
--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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________________________________
This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. This communication may contain protected health information (PHI) that is legally protected from inappropriate disclosure by the Privacy Standards of the Health Insurance Portability and Accountability Act (HIPAA) and relevant Pennsylvania Laws. You can direct questions concerning PHI or HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If you are not the intended recipient, please note that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this message in error, you should notify the sender immediately by telephone or by return e-mail and delete and destroy all copies of this message.
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|
awesome. :-)
Thanks! and best of luck going forward
…On Tue, Sep 15, 2020 at 1:43 PM foxchase ***@***.***> wrote:
Hi Brian,
I did what you asked, and it went well, no Traceback now.
Thank you
________________________________
From: Brian Haas ***@***.***>
Sent: Tuesday, September 15, 2020 12:45 PM
To: NCIP/ctat-mutations ***@***.***>
Cc: Pei, Jianming ***@***.***>; Author <
***@***.***>
Subject: Re: [NCIP/ctat-mutations] UnicodeDecodeError: 'utf-8' codec can't
decode byte 0xe9 in position 6346: invalid continuation byte (#60)
EXTERNAL MESSAGE. DO NOT open attachments or click links from unknown
senders or unknown emails.
________________________________
Hi,
Can you do me a favor and update this code in your installation?
https://github.com/NCIP/ctat-mutations/blob/devel/PyLib/ctat_util.py
This should hopefully solve that error, and if you rerun the original job,
it should pick up where it left off.
thanks,
~brian
On Tue, Sep 15, 2020 at 12:07 PM foxchase ***@***.***>
wrote:
> Dear ctat-mutations developers,
> I tested the demo data and everything went well. when I tried my own data
> I got two Traceback errors at almost the final stage:
> 2020-09-15 11:39:07,731: INFO Pipeliner.Pipeliner.run_cmd Running:
> /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
> Traceback (most recent call last):
> File
> "/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py",
> line 47, in
> for line in hndl_vcf:
> File "/home/jpei/anaconda3/lib/python3.7/codecs.py", line 322, in decode
> (result, consumed) = self._buffer_decode(data, self.errors, final)
> UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position
6346:
> invalid continuation byte
> 2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run_cmd Error: Command
> '/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf'
> returned non-zero exit status 1., exit val: 1
> 2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run Error, command: [
> /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
> ] failed, stack trace: [ st:
>
file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py,
> lineno:86
> st: file:./ctat_mutations, lineno:1364
> st: file:./ctat_mutations, lineno:2816
> ]
> Traceback (most recent call last):
> File "./ctat_mutations", line 2824, in
> pipeliner.run()
> File
>
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py",
> line 71, in run
> cmd.run(checkpoint_dir)
> File
>
"/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py",
> line 132, in run
> raise RuntimeError(errmsg)
> RuntimeError: Error, command: [
> /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf
>
/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
> ] failed, stack trace: [ st:
>
file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py,
> lineno:86
> st: file:./ctat_mutations, lineno:1364
> st: file:./ctat_mutations, lineno:2816
> ]
>
> Thank you for your effort.
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#60>, or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/ABZRKX5VBN7SNWWFL7WOUJLSF6GKNANCNFSM4RNLTG3A
>
> .
>
--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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________________________________
This electronic message is intended to be for the use of the named
recipient, and may contain information that is confidential or privileged.
This communication may contain protected health information (PHI) that is
legally protected from inappropriate disclosure by the Privacy Standards of
the Health Insurance Portability and Accountability Act (HIPAA) and
relevant Pennsylvania Laws. You can direct questions concerning PHI or
HIPAA to the Corporate Compliance and Privacy Officer at (215) 707-5605. If
you are not the intended recipient, please note that any dissemination,
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you have received this message in error, you should notify the sender
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The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
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Dear ctat-mutations developers,
I tested the demo data and everything went well. when I tried my own data I got two Traceback errors at almost the final stage:
2020-09-15 11:39:07,731: INFO Pipeliner.Pipeliner.run_cmd Running: /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf
Traceback (most recent call last):
File "/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py", line 47, in
for line in hndl_vcf:
File "/home/jpei/anaconda3/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 6346: invalid continuation byte
2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run_cmd Error: Command '/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf' returned non-zero exit status 1., exit val: 1
2020-09-15 11:39:07,847: ERROR Pipeliner.Pipeliner.run Error, command: [ /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf ] failed, stack trace: [ st: file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py, lineno:86
st: file:./ctat_mutations, lineno:1364
st: file:./ctat_mutations, lineno:2816
]
Traceback (most recent call last):
File "./ctat_mutations", line 2824, in
pipeliner.run()
File "/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py", line 71, in run
cmd.run(checkpoint_dir)
File "/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py", line 132, in run
raise RuntimeError(errmsg)
RuntimeError: Error, command: [ /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/src/groom_vcf.py /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/variants.HC_hard_cutoffs_applied.vcf /home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/output/work_dir/variants.pre_annot_filt.vcf ] failed, stack trace: [ st: file:/home/jpei/Desktop/NGS/ctat-mutations/ctat-mutations/PyLib/Pipeliner.py, lineno:86
st: file:./ctat_mutations, lineno:1364
st: file:./ctat_mutations, lineno:2816
]
Thank you for your effort.
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